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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PYRIMIDINE-NUCLEOSIDE PHOSPHORYLASE FROM STAPHYLOCOCCUS AUREUS
 
Authors :  I. A. Shumilin, M. Zimmerman, M. Cymborowski, T. Skarina, O. Onopriyen W. F. Anderson, A. Savchenko, W. Minor, Center For Structural Geno Infectious Diseases (Csgid)
Date :  22 Apr 09  (Deposition) - 26 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Glycosyltransferase, Transferase, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. A. Shumilin, M. Zimmerman, M. Cymborowski, T. Skarina, O. Onopriyenko, W. F. Anderson, A. Savchenko, W. Minor, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of A Putative Pyrimidine-Nucleoside Phosphorylase From Staphylococcus Aureus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIMIDINE-NUCLEOSIDE PHOSPHORYLASE
    Chains: A
    EC Number: 2.4.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19C
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDP, PYN, SACOL2128
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93062
    Strain: COL
    Synonym: PYNP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
3THM1Ligand/IonTHYMIDINE
Biological Unit 1 (3, 38)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
3THM2Ligand/IonTHYMIDINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:165 , ARG A:168 , ILE A:180 , SER A:183 , LYS A:187 , PHE A:207 , HOH A:698BINDING SITE FOR RESIDUE THM A 434
2AC2SOFTWAREARG A:245 , PRO A:265 , LYS A:266 , ASP A:267 , HOH A:442 , HOH A:538 , HOH A:690 , HOH A:756BINDING SITE FOR RESIDUE SO4 A 435
3AC3SOFTWARETHR A:92 , LYS A:108 , SER A:110 , THR A:120 , HOH A:616 , HOH A:699BINDING SITE FOR RESIDUE SO4 A 436

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H5Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H5Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H5Q)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMID_PHOSPHORYLASEPS00647 Thymidine and pyrimidine-nucleoside phosphorylases signature.PDP_STAAC110-125  1A:110-125
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMID_PHOSPHORYLASEPS00647 Thymidine and pyrimidine-nucleoside phosphorylases signature.PDP_STAAC110-125  2A:110-125

(-) Exons   (0, 0)

(no "Exon" information available for 3H5Q)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:436
 aligned with PDP_STAAC | Q5HE64 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:436
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427      
            PDP_STAAC     - ---MRMIDIIEKKRDGHTLTTEEINFFIGGYVKGDIPDYQASSLAMAIYFQDMNDDERAALTMAMVNSGDMIDLSDIKGVKVDKHSTGGVGDTTTLVLAPLVAAVDVPVAKMSGRGLGHTGGTIDKLEAIDGFHVEIDEATFVKLVNENKVAVVGQSGNLTPADKKLYALRDVTGTVNSIPLIASSIMSKKIAAGADAIVLDVKTGSGAFMKTLEDAEALAHAMVRIGNNVGRNTMAIISDMNQPLGRAIGNALELQEAIDTLKGQGPKDLTELVLTLGSQMVVLANKAETLEEARALLIEAINSGAALEKFKTFIKNQGGDETVIDHPERLPQAQYQIEYKAKKSGYVTELVSNDIGVASMMLGAGRLTKEDDIDLAVGIVLNKKIGDKVEEGESLLTIHSNRQDVDDVVKKLDSSITIADHVVSPTLIHKIITE 433
               SCOP domains d3h5qa1 A:-2-70 automated matches                                        d3h5qa2 A:71-330 automated matches                                                                                                                                                                                                                                  d3h5qa3 A:331-433 automated matches                                                                     SCOP domains
               CATH domains 3h5qA01 A:-2-67                                                       -3h5qA02 A:69-330,A:424-433 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                                                                                                                                     3h5qA03 A:331-423  [code=3.90.1170.30, no name defined]                                      3h5qA02    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..............eeeee......hhhhhhhhhhhhh...eeee.........hhhhhhh.........hhhhhhhhhhhhheeee......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhhhhh..eeeeeee.......eeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....eeeeee....eeeeeehhhhhhhhhhhh...............eeee......ee....eeeeeee....hhhhhhhhhhheeee........eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h5q A  -2 SNAmRmIDIIEKKRDGHTLTTEEINFFIGGYVKGDIPDYQASSLAmAIYFQDmNDDERVALTmAmVNSGDmIDLSDIKGVKVDKHSTGGVGDTTTLVLAPLVAAVDVPVAKmSGRGLGHTGGTIDKLEAIDGFHVEIDEATFVKLVNENKVAVVGQSGNLTPADKKLYALRDVTGTVNSIPLIASSImSKKIAAGADAIVLDVKTGSGAFmKTLEDAEALAHAmVRIGNNVGRNTmAIISDmNQPLGRAIGNALELQEAIDTLKGQGPKDLTELVLTLGSQmVVLANKAETLEEARALLIEAINSGAALEKFKTFIKNQGGDETVIDHPERLPQAQYQIEYKAKKSGYVTELVSNDIGVASmmLGAGRLTKEDDIDLAVGIVLNKKIGDKVEEGESLLTIHSNRQDVDDVVKKLDSSITIADHVVSPTLIHKIITE 433
                               | |   7        17        27        37     |  47  |     57  | |   67|       77        87        97       107 |     117       127       137       147       157       167       177       187       197       207|      217   |   227     | 237 |     247       257       267       277 |     287       297       307       317       327       337       347       357 ||    367       377       387       397       407       417       427      
                               | |                                      43-MSE 50-MSE    60-MSE   |                                      109-MSE                                                                     185-MSE                208-MSE      221-MSE     233-MSE |                                     279-MSE                                                                         359-MSE                                                                      
                               1-MSE                                                       62-MSE |                                                                                                                                                                        239-MSE                                                                                                                  360-MSE                                                                     
                                 3-MSE                                                           68-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H5Q)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (PDP_STAAC | Q5HE64)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004645    phosphorylase activity    Catalysis of the reaction: 1,4-alpha-D-glucosyl(n) + phosphate = 1,4-alpha-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate. The name should be qualified in each instance by adding the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, glycogen phosphorylase.
    GO:0016154    pyrimidine-nucleoside phosphorylase activity    Catalysis of the reaction: pyrimidine nucleoside + phosphate = pyrimidine + alpha-D-ribose 1-phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0006213    pyrimidine nucleoside metabolic process    The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).

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